Title |
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
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Published in |
Genome Biology, March 2023
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DOI | 10.1186/s13059-023-02877-1 |
Pubmed ID | |
Authors |
Marouen Ben Guebila, Tian Wang, Camila M. Lopes-Ramos, Viola Fanfani, Des Weighill, Rebekka Burkholz, Daniel Schlauch, Joseph N. Paulson, Michael Altenbuchinger, Katherine H. Shutta, Abhijeet R. Sonawane, James Lim, Genis Calderer, David G.P. van IJzendoorn, Daniel Morgan, Alessandro Marin, Cho-Yi Chen, Qi Song, Enakshi Saha, Dawn L. DeMeo, Megha Padi, John Platig, Marieke L. Kuijjer, Kimberly Glass, John Quackenbush |
Abstract |
Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is a collection of open-source methods to infer GRNs, conduct differential network analyses, estimate community structure, and explore the transitions between biological states. The netZoo builds on our ongoing development of network methods, harmonizing the implementations in various computing languages and between methods to allow better integration of these tools into analytical pipelines. We demonstrate the utility using multi-omic data from the Cancer Cell Line Encyclopedia. We will continue to expand the netZoo to incorporate additional methods. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 18 | 21% |
Norway | 6 | 7% |
India | 5 | 6% |
France | 5 | 6% |
China | 3 | 3% |
United Kingdom | 3 | 3% |
Spain | 2 | 2% |
Mexico | 2 | 2% |
Portugal | 1 | 1% |
Other | 10 | 11% |
Unknown | 32 | 37% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 44 | 51% |
Members of the public | 41 | 47% |
Practitioners (doctors, other healthcare professionals) | 1 | 1% |
Science communicators (journalists, bloggers, editors) | 1 | 1% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 29 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 6 | 21% |
Unspecified | 2 | 7% |
Researcher | 2 | 7% |
Student > Bachelor | 2 | 7% |
Student > Doctoral Student | 1 | 3% |
Other | 2 | 7% |
Unknown | 14 | 48% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 5 | 17% |
Agricultural and Biological Sciences | 4 | 14% |
Unspecified | 2 | 7% |
Physics and Astronomy | 1 | 3% |
Neuroscience | 1 | 3% |
Other | 0 | 0% |
Unknown | 16 | 55% |